The Twilight Jedi were founded by Jedi Master Kogun Shay in 90 ABY, having left the Jedi Council over a disagreement within it over the rise of Kol Skywalker, who he considered a danger to the Jedi. Moving himself and the families of any Jedi who agreed to him - very few - to Utapau, he consolidated his own Jedi, making use of light side and dark side powers, as the Twilight Jedi Order.

Kogun ended up aware of the One Sith, having encountered an agent of Vongerella, a Sith who worked with Darth Krayt. Maleficarum was discovered by the One Sith, and had to hide her links to Vongerella, as, on her masters direction, she was sabotaging One Sith links with the other Force groups, such as the Jensaarai and Korunnai.

On an excursion to find new apprentices on Haruun Kal the Twilight Grandmaster, Kogun fell across the One Sith task force chasing Maleficarum, saving her from the Sith. This action ingratiated her to him, but Kogun's vessel was destroyed. The two were forced to flee through the dangerous Highlands, a Sith relying upon a Twilight Jedi, and vice-versa. In those long days, the two bonded, and Maleficarum informed Kogun of the One Sith in their entirety - the thousands of Sith hiding on Korriban - and he realised that the Jedi couldn't be told of this information - the Order wasn't strong enough to attack Korriban in force, and involving the Alliance or Empire would take too much time.

As such, Kogun and Maleficarum came up with their own plan. Maleficarum hid in the forestry, and Kogun gave up himself to the Sith, as a prisoner, revealing the existence of the Twilight Jedi to Darth Krayt. His and Maleficarum's son was placed in the Empire, as a pawn that would eventually become an Imperial Knight named Eydan Skorne, and the Twilight Jedi taken by Darth Krayt as his own. Their families imprisoned, the Twilight Jedi did as they were told.

Krayt and the Sith Masters on Utapau transformed the Twilight Jedi into purely lightsiders, using them as fake Jedi to spread discontent and frame the Jedi for several actions involving assassinations across the Outer Rim, weakening support for the Alliance throughout it. Kogun Shay remained in Krayt's dungeons, until Maleficarum was sure the time was right to save him - Vongerella having confirmed his survival herself, taking command of the plan as her own.

The Twilight Jedi Simeon, however, plagued by terrible visions, went rogue in 127 ABY, nearly exposing the Order. Simeon ended up key to the creation of Darth Zorn, and also his subsequent death, but the ramifications became an issue for the Empire, damaging the Imperial Knights. Yuuzhan Vong agents of Vongerella - whom was directing Nas Choka in support of the Jedi and Alliance - freed Kogun Shay, and he faded into the shadows, preparing for his emergence alone.

Kogun Shay directed elements within the Twilight Jedi to prepare his earlier plans, as coordinated by the Maleficarum apprentice named Athame. When the Emperor and Grandmaster met, he and Vongerella discovered Krayt was to emerge then, and his Order at the Battle of Bastion simultaneously. He intervened, however, too early, disrupting the meeting and justifying the Sith intervention entirely - his lover Maleficarum joined him, the two of them seeking to kill the Emperor and ruin Krayt's efforts there and then - he and his own Sith engaging Kol Skywalker and Wolf Sazen in a horrific duel.

Kogun and Maleficarum were killed by Antares Draco and the Emperor, shattering the plan which had created three decades of suffering for the Twilight Jedi - but his sacrifice was not in vain. In the days after the Battle of Bastion, the Twilight Jedi overthrew the Sith on Utapau.

The Twilight Jedi joined the Utapaun's in preparing for warfare, taking their Dreadnaughts and fighter craft and forging them into a force to be reckoned with. The Empire and it's allies came down on Utapau hard, but the Twilight Jedi escaped, hooking up with the Templar Dade Leviathan and joining the main-stream Twilight Templars.